Shay Teaching wrote:
Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
trajectory and one mutant trajectory using the following command:
g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx
The file wt_backbone.ndx contains the backbone of the protein (Backbone
indices are identical between wt and mutant).
The result is that I am getting a well deserved error saying that wt.xtc
and mutant.xtc has different number of atoms (the tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one (76129 atoms)
So the question becomes: Is there a (convenient) way to produce
rms-matrix between wt and mutant?
Or perhaps circumvent this problem in some other way?
Use trjconv to write out new trajectories containing only backbone atoms of each
protein, then use tpbconv to write a .tpr file with only backbone atoms in it
(using index groups, if necessary). Then run g_rms again with these new
trajectories and .tpr file. Everything should match if the indices are chosen
correctly.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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